Also sometimes there is a delay when switching scenes, but not always.

I have a video in actor, movie actor and two projector actors as well as a keyboard watcher and eyes++ so its not a lot going on. The video is photo jpeg compression. I'm using my smaller machine but I have created way more complex things with it using Izzy 1 in the past without these things happening.

Are there changes to setups, file types, ect. that you guys are doing now that you're using 2.1?

Unfortunately Isadora 2.x was not heavaly tested on 10.8.5. There will come a few improvements for 10.8x with the next Isadora release, but besides that the new palyback engine (AVfoundation) was not fully mature until 10.9. Your would benefit with a more stable experience upgrading to 10.9.